Strepsiptera, phylogenomics and the long branch attraction problem

First genome assembly of the order Strepsiptera using PacBio HiFi reads reveals a miniature genome

Twisted-wing insects (Strepsiptera) are an enigmatic order of parasites with unusual life histories and striking sexual dimorphism. Males emerge from hosts as free-living winged adults, while females from most species remain as endoparasites that retain larval traits. Due to scarce genomic data and phylogenetic controversies, Strepsiptera was only recently placed as the closest living relative to beetles (Coleoptera). Here, we report the first PacBio HiFi genome assembly of the strepsipteran Xenos peckii (Xenidae). This de novo assembly size is 72.1 Mb, with a BUSCO score of 87.4%, N50 of 7.3 Mb, 23.4% GC content, and 38.41% repeat content. We identified 8 contigs that contain >75% of the assembly and reflect the haploid chromosome number reported from karyotypic data, and 3 contigs that exhibit sex chromosome coverage patterns. Additionally, the mitochondrial genome is 16,111 bp long and has 37 genes. This long-read assembly for Strepsiptera reveals a miniature genome and provides a unique tool to understand complex genome evolution associated with a parasitic lifestyle and extreme sexual dimorphism.

Phylogenomic analysis of Stylops reveals the evolutionary history of a Holarctic Strepsiptera radiation parasitizing wild bees

Holarctic Stylops is the largest genus of the enigmatic insect order Strepsiptera, twisted winged parasites. Members of Stylops are obligate endoparasites of Andrena mining bees and exhibit extreme sexual dimorphism typical of Strepsiptera. So far, molecular studies on Stylops have focused on questions on species delimitation. Here, we utilize the power of whole genome sequencing to infer the phylogeny of this morphologically challenging genus from thousands of loci. We use a species tree method, concatenated maximum likelihood analysis and Bayesian analysis with a relaxed clock model to reconstruct the phylogeny of 46 Stylops species, estimate divergence times, evaluate topological consistency across methods and infer the root position. Furthermore, the biogeographical history and coevolutionary patterns with host species are assessed. All methods recovered a well resolved topology with close to all nodes maximally supported and only a handful of minor topological variations. Based on the result, we find that included species can be divided into 12 species groups, seven of them including only Palaearctic species, three Nearctic and two were geographically mixed. We find a strongly supported root position between a clade formed by the spreta, thwaitesi and gwynanae species groups and the remaining species and that the sister group of Stylops is Eurystylops or Eurystylops + Kinzelbachus. Our results indicate that Stylops originated in the Western Palaearctic or Western Palaearctic and Nearctic in the early Neogene or late Paleogene, with four independent dispersal events to the Nearctic. Cophylogenetic analyses indicate that the diversification of Stylops has been shaped by both significant coevolution with the mining bee hosts and host-shifting. The well resolved and strongly supported phylogeny will provide a valuable phylogenetic basis for further studies into the fascinating world of Strepsipterans.

Learning From an Artificial Neural Network in Phylogenetics

We show that an iterative ansatz of deep learning and human intelligence guided simplification may lead to surprisingly simple solutions for a difficult problem in phylogenetics. Distinguishing Farris and Felsenstein trees is a longstanding problem in phylogenetic tree reconstruction. The Artificial Neural Network F-zoneNN solves this problem for 4-taxon alignments evolved under the Jukes-Cantor model. It distinguishes between Farris and Felsenstein trees, but owing to its complexity, lacks transparency in its mechanism of discernment. Based on the simplification of F-zoneNN and alignment properties we constructed the function FarFelDiscerner. In contrast to F-zoneNN, FarFelDiscerner's decision process is understandable. Moreover, FarFelDiscerner is significantly simpler than F-zoneNN. Despite its simplicity this function infers the tree-type almost perfectly on noise-free data, and also performs well on simulated noisy alignments of finite length. We applied FarFelDiscerner to the historical Holometabola alignments where it places Strepsiptera with beetles, concordant with the current scientific view.

The Chalcidoidea bush of life: evolutionary history of a massive radiation of minute wasps

Chalcidoidea are mostly parasitoid wasps that include as many as 500 000 estimated species. Capturing phylogenetic signal from such a massive radiation can be daunting. Chalcidoidea is an excellent example of a hyperdiverse group that has remained recalcitrant to phylogenetic resolution. We combined 1007 exons obtained with Anchored Hybrid Enrichment with 1048 ultra-conserved elements (UCEs) for 433 taxa including all extant families, >95% of all subfamilies, and 356 genera chosen to represent the vast diversity of the superfamily. Going back and forth between the molecular results and our collective knowledge of morphology and biology, we detected bias in the analyses that was driven by the saturation of nucleotide data. Our final results are based on a concatenated analysis of the least saturated exons and UCE datasets (2054 loci, 284 106 sites). Our analyses support an expected sister relationship with Mymarommatoidea. Seven previously recognized families were not monophyletic, so support for a new classification is discussed. Natural history in some cases would appear to be more informative than morphology, as illustrated by the elucidation of a clade of plant gall associates and a clade of taxa with planidial first-instar larvae. The phylogeny suggests a transition from smaller soft-bodied wasps to larger and more heavily sclerotized wasps, with egg parasitism as potentially ancestral for the entire superfamily. Deep divergences in Chalcidoidea coincide with an increase in insect families in the fossil record, and an early shift to phytophagy corresponds with the beginning of the "Angiosperm Terrestrial Revolution". Our dating analyses suggest a middle Jurassic origin of 174 Ma (167.3-180.5 Ma) and a crown age of 162.2 Ma (153.9-169.8 Ma) for Chalcidoidea. During the Cretaceous, Chalcidoidea may have undergone a rapid radiation in southern Gondwana with subsequent dispersals to the Northern Hemisphere. This scenario is discussed with regard to knowledge about the host taxa of chalcid wasps, their fossil record and Earth's palaeogeographic history.

A generic classification of Xenidae (Strepsiptera) based on the morphology of the female cephalothorax and male cephalotheca with a preliminary checklist of species

The generic taxonomy and host specialization of Xenidae have been understood differently by previous authors. Although the recent generic classification has implied a specialization on the level of host families or subfamilies, the hypothesis that each xenid genus is specialized to a single host genus was also previously postulated. A critical evaluation of the classification of the genera of Xenidae is provided here based on morphology in accordance with results of recent molecular phylogenetic studies. External features of the female cephalothoraces and male cephalothecae were documented in detail with different techniques. Diagnoses and descriptions are presented for all 13 delimited genera. The earliest diverging genera are usually well characterized by unique features, whereas deeply nested genera are usually characterized by combinations of characters. Three new genera are described: Sphecixenosgen. nov., Tuberoxenosgen. nov., and Deltoxenosgen. nov. Five previously described genera are removed from synonymy: Tachytixenos Pierce, 1911, stat. res.; Brasixenos Kogan & Oliveira, 1966, stat. res.; Leionotoxenos Pierce, 1909, stat. res.; Eupathocera Pierce, 1908, stat. res.; and Macroxenos Schultze, 1925, stat. res. One former subgenus is elevated to generic rank: Nipponoxenos Kifune & Maeta, 1975, stat. res.Monobiaphila Pierce, 1909, syn. nov. and Montezumiaphila Brèthes, 1923, syn. nov. are recognized as junior synonyms of Leionotoxenos Pierce, 1909, stat. res.Ophthalmochlus Pierce, 1908, syn. nov., Homilops Pierce, 1908, syn. nov., Sceliphronechthrus Pierce, 1909, syn. nov., and Ophthalmochlus (Isodontiphila) Pierce, 1919, syn. nov. are recognized as junior synonyms of Eupathocera Pierce, 1908, stat. res. A preliminary checklist of 119 described species of Xenidae with information on their hosts and distribution is provided. The following 14 species are recognized as valid and restituted from synonymy: Tachytixenos indicus Pierce, 1911, stat. res.; Brasixenos acinctus Kogan & Oliveira, 1966, stat. res.; Brasixenos araujoi (Oliveira & Kogan, 1962), stat. res.; Brasixenos bahiensis Kogan & Oliveira, 1966, stat. res.; Brasixenos brasiliensis Kogan & Oliveira, 1966, stat. res.; Brasixenos fluminensis Kogan & Oliveria, 1966, stat. res.; Brasixenos myrapetrus Trois, 1988, stat. res.; Brasixenos zikani Kogan & Oliveira, 1966, stat. res.; Leionotoxenos hookeri Pierce, 1909, stat. res.; Leionotoxenos jonesi Pierce, 1909, stat. res.; Leionotoxenos louisianae Pierce, 1909, stat. res.; Eupathocera luctuosae Pierce, 1911, stat. res.; Eupathocera lugubris Pierce, 1909, stat. res.; Macroxenos piercei Schultze, 1925, stat. res. New generic combinations are proposed for 51 species: Leionotoxenos arvensidis (Pierce, 1911), comb. nov.; Leionotoxenos bishoppi (Pierce, 1909), comb. nov.; Leionotoxenos foraminati (Pierce, 1911), comb. nov.; Leionotoxenos fundati (Pierce, 1911), comb. nov.; Leionotoxenos huastecae (Székessy, 1965), comb. nov.; Leionotoxenos itatiaiae (Trois, 1984), comb. nov.; Leionotoxenos neomexicanus (Pierce, 1919), comb. nov.; Leionotoxenos prolificum (Teson & Remes Lenicov, 1979), comb. nov.; Leionotoxenos robertsoni (Pierce, 1911), comb. nov.; Leionotoxenos tigridis (Pierce, 1911), comb. nov.; Leionotoxenos vigili (Brèthes, 1923), comb. nov.; Eupathocera argentina (Brèthes, 1923), comb. nov.; Eupathocera auripedis (Pierce, 1911), comb. nov.; Eupathocera bucki (Trois, 1984), comb. nov.; Eupathocera duryi (Pierce, 1909), comb. nov.; Eupathocera erynnidis (Pierce, 1911), comb. nov.; Eupathocera fasciati (Pierce, 1909), comb. nov.; Eupathocera fuliginosi (Brèthes, 1923), comb. nov.; Eupathocera inclusa (Oliveira & Kogan, 1963), comb. nov.; Eupathocera insularis (Kifune, 1983), comb. nov.; Eupathocera mendozae (Brèthes, 1923), comb. nov.; Eupathocera piercei (Brèthes, 1923), comb. nov.; Eupathocera striati (Brèthes, 1923), comb. nov.; Eupathocera taschenbergi (Brèthes, 1923), comb. nov.; Eupathocera westwoodii (Templeton, 1841), comb. nov.; Macroxenos papuanus (Székessy, 1956), comb. nov.; Sphecixenos abbotti (Pierce, 1909), comb. nov.; Sphecixenos astrolabensis (Székessy, 1956), comb. nov.; Sphecixenos dorae (Luna de Carvalho, 1956), comb. nov.; Sphecixenos erimae (Székessy, 1956), comb. nov.; Sphecixenos esakii (Hirashima & Kifune, 1962), comb. nov.; Sphecixenos gigas (Pasteels, 1950), comb. nov.; Sphecixenos kurosawai (Kifune, 1984), comb. nov.; Sphecixenos laetum (Ogloblin, 1926), comb. nov.; Sphecixenos orientalis (Kifune, 1985), comb. nov.; Sphecixenos reticulatus (Luna de Carvalho, 1972), comb. nov.; Sphecixenos simplex (Székessy, 1956), comb. nov.; Sphecixenos vanderiisti (Pasteels, 1952), comb. nov.; Tuberoxenos altozambeziensis (Luna de Carvalho, 1959), comb. nov.; Tuberoxenos sinuatus (Pasteels, 1956), comb. nov.; Tuberoxenos sphecidarum (Siebold, 1839), comb. nov.; Tuberoxenos teres (Pasteels, 1950), comb. nov.; Tuberoxenos tibetanus (Yang, 1981), comb. nov.; Deltoxenos bequaerti (Luna de Carvalho, 1956), comb. nov.; Deltoxenos bidentatus (Pasteels, 1950), comb. nov.; Deltoxenos hirokoae (Kifune & Yamane, 1992), comb. nov.; Deltoxenos iwatai (Esaki, 1931), comb. nov.; Deltoxenos lusitanicus (Luna de Carvalho, 1960), comb. nov.; Deltoxenos minor (Kifune & Maeta, 1978), comb. nov.; Deltoxenos rueppelli (Kinzelbach, 1971a), comb. nov.; Xenos ropalidiae (Kinzelbach, 1975), comb. nov.Xenos minor Kinzelbach, 1971a, syn. nov. is recognized as a junior synonym of X. vesparum Rossi, 1793. Ophthalmochlus duryi Pierce, 1908, nomen nudum and Eupathocera lugubris Pierce, 1908, nomen nudum are recognized as nomina nuda and therefore unavailable in zoological nomenclature. The species diversity of Xenidae probably remains poorly known: the expected number of species is at least twice as high as the number presently described.

The evolution of insect biodiversity

Insects comprise over half of all described animal species. Together with the Protura (coneheads), Collembola (springtails) and Diplura (two-pronged bristletails), insects form the Hexapoda, a terrestrial arthropod lineage characterised by possessing six legs. Exponential growth of genome-scale data for the hexapods has substantially altered our understanding of the origin and evolution of insect biodiversity. Phylogenomics has provided a new framework for reconstructing insect evolutionary history, resolving their position among the arthropods and some long-standing internal controversies such as the placement of the termites, twisted-winged insects, lice and fleas. However, despite the greatly increased size of phylogenomic datasets, contentious relationships among key insect clades remain unresolved. Further advances in insect phylogeny cannot rely on increased depth and breadth of genome and taxon sequencing. Improved modelling of the substitution process is fundamental to countering tree-reconstruction artefacts, while gene content, modelling of duplications and deletions, and comparative morphology all provide complementary lines of evidence to test hypotheses emerging from the analysis of sequence data. Finally, the integration of molecular and morphological data is key to the incorporation of fossil species within insect phylogeny. The emerging integrated framework of insect evolution will help explain the origins of insect megadiversity in terms of the evolution of their body plan, species diversity and ecology. Future studies of insect phylogeny should build upon an experimental, hypothesis-driven approach where the robustness of hypotheses generated is tested against increasingly realistic evolutionary models as well as complementary sources of phylogenetic evidence.

Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea)

Recent technical advances combined with novel computational approaches have promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be paid to potential analytical bias. We present the first molecular phylogenetic hypothesis for the family Chalcididae, a group of parasitoid wasps, with a representative sampling (144 ingroups and seven outgroups) that covers all described subfamilies and tribes, and 82% of the known genera. Analyses of 538 Ultra-Conserved Elements (UCEs) with supermatrix (RAxML and IQTREE) and gene tree reconciliation approaches (ASTRAL, ASTRID) resulted in highly supported topologies in overall agreement with morphology but reveal conflicting topologies for some of the deepest nodes. To resolve these conflicts, we explored the phylogenetic tree space with clustering and gene genealogy interrogation methods, analyzed marker and taxon properties that could bias inferences and performed a thorough morphological analysis (130 characters encoded for 40 taxa representative of the diversity). This joint analysis reveals that UCEs enable attainment of resolution between ancestry and convergent/divergent evolution when morphology is not informative enough, but also shows that a systematic exploration of bias with different analytical methods and a careful analysis of morphological features is required to prevent publication of artifactual results. We highlight a GC content bias for maximum-likelihood approaches, an artifactual mid-point rooting of the ASTRAL tree and a deleterious effect of high percentage of missing data (>85% missing UCEs) on gene tree reconciliation methods. Based on the results we propose a new classification of the family into eight subfamilies and ten tribes that lay the foundation for future studies on the evolutionary history of Chalcididae.

Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)

Despite many attempts in the Sanger sequencing era, the phylogeny of fig trees remains unresolved, which limits our ability to analyze the evolution of key traits that may have contributed to their evolutionary and ecological success. We used restriction-site-associated DNA sequencing (c. 420 kb) and 102 morphological characters to elucidate the relationships between 70 species of Ficus. To increase phylogenetic information for higher-level relationships, we targeted conserved regions and assembled paired reads into long loci to enable the retrieval of homologous loci in outgroup genomes. We compared morphological and molecular results to highlight discrepancies and reveal possible inference bias. For the first time, we recovered a monophyletic subgenus Urostigma (stranglers) and a clade with all gynodioecious Ficus. However, we show, with a new approach based on iterative principal component analysis, that it is not (and will probably never be) possible to homogenize evolutionary rates and GC content for all taxa before phylogenetic inference. Four competing positions for the root of the molecular tree are possible. The placement of section Pharmacosycea as sister to other fig trees is not supported by morphological data and considered a result of a long-branch attraction artefact to the outgroups. Regarding morphological features and indirect evidence from the pollinator tree of life, the topology that divides Ficus into monoecious versus gynodioecious species appears most plausible. It seems most likely that the ancestor of fig trees was a freestanding tree and active pollination is inferred as the ancestral state, contrary to previous hypotheses. However, ambiguity remains on the ancestral breeding system. Despite morphological plasticity, we advocate restoring a central role to morphology in our understanding of the evolution of Ficus, as it can help detect systematic errors that appear more pronounced with larger molecular datasets.

On the value of Burmese amber for understanding insect evolution: Insights from †Heterobathmilla - an exceptional stem group genus of Strepsiptera (Insecta)

Burmese amber and amber from other periods and regions became a rich source of new extinct insect species and yielded important insights in insect evolution in the dimension of time. Amber fossils have contributed to the understanding of the phylogeny, biology, and biogeography of insects and other groups, and have also gained great importance for dating molecular trees. Another major potential is the documentation of faunal, floral and climatic shifts. Evolutionary transitions can be well-documented in amber fossils and can reveal anatomical transformations and the age of appearance of structural features. Here, using a new stem group species of Strepsiptera from Burmite, we evaluate this potential of amber insect fossils to assess the current phylogeny of Strepsiptera, with the main emphasis on the early splitting events in the stem group. Amber fossils have greatly contributed to the understanding of the evolution of Strepsiptera in the late Mesozoic and the Cenozoic. †Heterobathmilla kakopoios Pohl and Beutel gen. et sp. n. described here is placed in the stem group of the order, in a clade with †Kinzelbachilla (†Kinzelbachillidae) and †Phthanoxenos (†Phthanoxenidae). †Phthanoxenidae has priority over †Kinzelbachillidae, and the latter is synonymised. The superb details available from this new fossil allowed us to explore unique features of the antennae, mouthparts, and male copulatory apparatus, and to provide a phylogenetic hypothesis for the order. The younger †Protoxenos from Eocene Baltic amber was confirmed as sister to all remaining extinct and extant groups of Strepsiptera, whereas the position of the Cretaceous †Cretostylops in the stem group remains ambivalent. While the value of Burmite and amber from other periods has a recognized impact on our knowledge of the evolution in various lineages, this new fossil does not fundamentally change our picture of the phylogeny and evolution of early Strepsiptera. However, it offers new insights into the morphological diversity in the early evolution of the group.

Distinguishing Felsenstein Zone from Farris Zone Using Neural Networks

Maximum likelihood and maximum parsimony are two key methods for phylogenetic tree reconstruction. Under certain conditions, each of these two methods can perform more or less efficiently, resulting in unresolved or disputed phylogenies. We show that a neural network can distinguish between four-taxon alignments that were evolved under conditions susceptible to either long-branch attraction or long-branch repulsion. When likelihood and parsimony methods are discordant, the neural network can provide insight as to which tree reconstruction method is best suited to the alignment. When applied to the contentious case of Strepsiptera evolution, our method shows robust support for the current scientific view, that is, it places Strepsiptera with beetles, distant from flies.

The endoparasitic larval stages of Eoxenos laboulbenei: An atypical holometabolan development (Strepsiptera, Mengenillidae)

Endoparasitic larval stages of Eoxenos laboulbenei were documented with different techniques, with a main focus on the male tertiary larva. Two discrete endoparasitic stages occur, the secondary and the tertiary larva. The presence of large compound eyes and externally visible wing buds in the tertiary larva is a unique feature within Holometabola. The brain with large optic lobes is followed by a single postcephalic ganglionic complex. The cephalic musculature is greatly reduced but pharyngeal dilators and muscles associated with the mouth field are present. Postcephalic sclerites are absent except for the pronotum. The segmented legs bear filiform pretarsal claws. The indirect flight muscles fill up a large part of the metathorax. The 10-segmented abdomen lacks appendages. Pleural folds are present on the thorax and abdomen. The digestive tract is characterized by a very short oesophagus. The large midgut and the narrow hindgut are disconnected. Six short Malpighian tubules are present. Large testes fill out almost the entire abdomen. In contrast to the tertiary larva, the muscles of the secondary larva are not fully differentiated. Cephalic appendages are present as bud-shaped anlagen. The legs lack a pretarsal claw. The developmental transformations are outlined and discussed, also with respect to phylogenetic implications.

The Mitochondrial Genomes of Neuropteridan Insects and Implications for the Phylogeny of Neuroptera

The higher-level phylogeny of Neuroptera is explored here based on the newly determined mitochondrial genomic data, with a special focus on the interfamilial relationships of this group. Despite considerable progress in our understanding of neuropteran relationships, several mutually exclusive hypotheses have come out according to morphology-based analyses and molecular sequence data. The evaluation of these hypotheses is hampered by the limited taxonomic coverage of previous studies. In this paper, we sequenced four mitochondrial genomes to improve the taxonomic sampling for families: Myrmeleontidae, Ascalaphidae and outgroup Corydalidae. Phylogenetic analyses were run using various inference methods to (1) confirm that Coniopterygidae is sister to all other Neuroptera; (2) place Hemerobiidae as sister to Chrysopidae; (3) support the monophyly of Myrmeleontiformia and define its interfamilial relationships; and (4) recover Myrmeleontidae as paraphyletic due to the nested Ascalaphidae.

Effects of miniaturization in primary larvae of Strepsiptera (Insecta)

In this review the presently available morphological data on primary larvae of Strepsiptera are interpreted with respect to effects of miniaturization, but also their possible functional or phylogenetic background. The morphology of the 1st instars is mainly affected by functional constraints linked with parasitism but also by very distinct effects of miniaturization. The latter include modifications of the cephalic cuticle, the extremely limited free space in the body lumen, the shift of origins of cephalic muscles to the thorax, a reduced number of cephalic and thoracic muscles, extensions of muscles with cell bodies and other organelles, and an extreme concentration of the entire central nervous system in the middle region of the body. Pad-like adhesive structures on the distal leg segment and the abdominal jumping apparatus are clearly linked with the necessity to attach to a potential host but would not function in distinctly larger organisms.

Differential expression of the adult specifier E93 in the strepsipteran Xenos vesparum Rossi suggests a role in female neoteny

Holometaboly is a key evolutionary innovation that has facilitated the spectacular radiation of insects. Despite the undeniable advantage of complete metamorphosis, the female of some holometabolous species have lost the typical holometabolous development through neoteny. In Xenos vesparum Rossi (Strepsiptera: Stylopidae), a derived species of the holometabolous endoparasitic order Strepsiptera, neotenic females reach sexual maturity without the pupal and the imaginal stages, thus retaining their larval morphology (with the exception of the anterior part of the body or cephalothorax), while males undergo normal pupal-based metamorphosis. Expression of the “adult-specifier” E93 factor has been shown to be required for proper metamorphosis in holometabolous insects. Here, we investigated the involvement of E93 in female neoteny by cloning XvE93. Interestingly, while we detected a clear up-regulation of XvE93 expression in pupal and adult stages of males, persistent low levels of XvE93 were detected in X. vesparum females. However, a specific up-regulation of XvE93 was observed in the cephalothorax of late 4^th female instar larva, which correlates with the occurrence of neotenic-specific features in the anterior part of the female body. Moreover, the same expression dynamic in the cephalothorax and abdomen was also observed for other two critical metamorphic regulators, the anti-metamorphic XvKr-h1 and the pupal specifier XvBr-C. The specific up-regulation of XvE93 and XvBr-C in the female cephalothorax seems to be the result of an increase in 20-hydroxyecdysone (20E) signaling in this region for we detected higher expression levels of the 20E-dependent nuclear receptors XvHR3 and XvE75 in the cephalothorax. Overall, our results detect a sex-specific expression pattern of critical metamorphic genes in X. vesparum, suggesting that neoteny in Strepsiptera results from the modification of the normal expression of E93, Br-C and Kr-h1 genes.

Multispecies coalescent analysis confirms standing phylogenetic instability in Hexapoda

The multispecies coalescent (MSC) has been increasingly used in phylogenomic analyses due to the accommodation of gene tree topological heterogeneity by taking into account population-level processes, such as incomplete lineage sorting. In this sense, the phylogeny of insect species, which are characterized by their large effective population sizes, is suitable for a coalescent-based analysis. Furthermore, studies so far recovered short internal branches at early divergences of the insect tree of life, indicating fast evolutionary radiations that increase the probability of incomplete lineage sorting in deep time. Here, we investigated the performance of the MSC for a phylogenomic data set of hexapods compiled by Misof et al. (2014, Science 346:763). Our analysis recovered the monophyly of most insect orders, and major phylogenetic relationships were in agreement with current insect systematics. We identified, however, some evolutionary associations that were consistently problematic. Most noticeable, Hexapod monophyly was disrupted by the sister group relationship between the remiped crustacean and Insecta. Additionally, the interordinal relationships within Polyneoptera and Neuropteroidea were found to be phylogenetically unstable. We show that these controversial phylogenetic arrangements were also poorly supported by previous analyses, and therefore, we evaluated their robustness to stochastic errors from sampling sites and terminals, confirming standing problems in hexapod phylogeny in the genomics age.

Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction

Species tree reconstruction from genome-wide data is increasingly being attempted, in most cases using a two-step approach of first estimating individual gene trees and then summarizing them to obtain a species tree. The accuracy of this approach, which promises to account for gene tree discordance, depends on the quality of the inferred gene trees. At the same time, phylogenomic and phylotranscriptomic analyses typically use involved bioinformatics pipelines for data preparation. Errors and shortcomings resulting from these preprocessing steps may impact the species tree analyses at the other end of the pipeline. In this article, we first show that the presence of fragmentary data for some species in a gene alignment, as often seen on real data, can result in substantial deterioration of gene trees, and as a result, the species tree. We then investigate a simple filtering strategy where individual fragmentary sequences are removed from individual genes but the rest of the gene is retained. Both in simulations and by reanalyzing a large insect phylotranscriptomic data set, we show the effectiveness of this simple filtering strategy.

Fossil record of stem groups employed in evaluating the chronogram of insects (Arthropoda: Hexapoda)

Insecta s. str. (=Ectognatha), comprise the largest and most diversified group of living organisms, accounting for roughly half of the biodiversity on Earth. Understanding insect relationships and the specific time intervals for their episodes of radiation and extinction are critical to any comprehensive perspective on evolutionary events. Although some deeper nodes have been resolved congruently, the complete evolution of insects has remained obscure due to the lack of direct fossil evidence. Besides, various evolutionary phases of insects and the corresponding driving forces of diversification remain to be recognized. In this study, a comprehensive sample of all insect orders was used to reconstruct their phylogenetic relationships and estimate deep divergences. The phylogenetic relationships of insect orders were congruently recovered by Bayesian inference and maximum likelihood analyses. A complete timescale of divergences based on an uncorrelated log-normal relaxed clock model was established among all lineages of winged insects. The inferred timescale for various nodes are congruent with major historical events including the increase of atmospheric oxygen in the Late Silurian and earliest Devonian, the radiation of vascular plants in the Devonian, and with the available fossil record of the stem groups to various insect lineages in the Devonian and Carboniferous.

Progress, pitfalls and parallel universes: a history of insect phylogenetics

The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985-2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed.

Traumatic insemination and female counter-adaptation in Strepsiptera (Insecta)

In a few insect groups, males pierce the female's integument with their penis during copulation to transfer sperm. This so-called traumatic insemination was previously confirmed for Strepsiptera but only in species with free-living females. The more derived endoparasitic groups (Stylopidia) were suggested to exhibit brood canal mating. Further, it was assumed that females mate once and that pheromone production ceases immediately thereafter. Here we examined Stylops ovinae to provide details of the mating behaviour within Stylopidia. By using μCT imaging of Stylops in copula, we observed traumatic insemination and not, as previously suggested, brood canal mating. The penis is inserted in an invagination of the female cephalothorax and perforates its cuticle. Further we show that female Stylops are polyandrous and that males detect the mating status of the females. Compared to other strepsipterans the copulation is distinctly prolonged. This may reduce the competition between sperm of the first mating male with sperm from others. We describe a novel paragenital organ of Stylops females, the cephalothoracic invagination, which we suggest to reduce the cost of injuries. In contrast to previous interpretations we postulate that the original mode of traumatic insemination was maintained after the transition from free-living to endoparasitic strepsipteran females.

The analysis of Gene Regulatory Networks in plant evo-devo

We provide an overview of methods and workflows that can be used to investigate the topologies of Gene Regulatory Networks (GRNs) in the context of plant evolutionary-developmental (evo-devo) biology. Many of the species that occupy key positions in plant phylogeny are poorly adapted as laboratory models and so we focus here on techniques that can be efficiently applied to both model and non-model species of interest to plant evo-devo. We outline methods that can be used to describe gene expression patterns and also to elucidate the transcriptional, post-transcriptional, and epigenetic regulatory mechanisms underlying these patterns, in any plant species with a sequenced genome. We furthermore describe how the technique of Protein Resurrection can be used to confirm inferences on ancestral GRNs and also to provide otherwise-inaccessible points of reference in evolutionary histories by exploiting paralogues generated in gene and whole genome duplication events. Finally, we argue for the better integration of molecular data with information from paleobotanical, paleoecological, and paleogeographical studies to provide the fullest possible picture of the processes that have shaped the evolution of plant development.

Phylotranscriptomic Analysis Based on Coalescence was Less Influenced by the Evolving Rates and the Number of Genes: A Case Study in Ericales

Advances in high-throughput sequencing have generated a vast amount of transcriptomic data that are being increasingly used in phylogenetic reconstruction. However, processing the vast datasets for a huge number of genes and even identifying optimal analytical methodology are challenging. Through de novo sequenced and retrieved data from public databases, we identified 221 orthologous protein-coding genes to reconstruct the phylogeny of Ericales, an order characterized by rapid ancient radiation. Seven species representing different families in Ericales were used as in-groups. Both concatenation and coalescence methods yielded the same well-supported topology as previous studies, with only two nodes conflicting with previously reported relationships. The results revealed that a partitioning strategy could improve the traditional concatenation methodology. Rapidly evolving genes negatively affected the concatenation analysis, while slowly evolving genes slightly affected the coalescence analysis. The coalescence methods usually accommodated rate heterogeneity better and required fewer genes to yield well-supported topologies than the concatenation methods with both real and simulated data.

Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa

BACKGROUND

Understanding the phylogenetic relationships among major lineages of multicellular animals (the Metazoa) is a prerequisite for studying the evolution of complex traits such as nervous systems, muscle tissue, or sensory organs. Transcriptome-based phylogenies have dramatically improved our understanding of metazoan relationships in recent years, although several important questions remain. The branching order near the base of the tree, in particular the placement of the poriferan (sponges, phylum Porifera) and ctenophore (comb jellies, phylum Ctenophora) lineages is one outstanding issue. Recent analyses have suggested that the comb jellies are sister to all remaining metazoan phyla including sponges. This finding is surprising because it suggests that neurons and other complex traits, present in ctenophores and eumetazoans but absent in sponges or placozoans, either evolved twice in Metazoa or were independently, secondarily lost in the lineages leading to sponges and placozoans.

RESULTS

To address the question of basal metazoan relationships we assembled a novel dataset comprised of 1080 orthologous loci derived from 36 publicly available genomes representing major lineages of animals. From this large dataset we procured an optimized set of partitions with high phylogenetic signal for resolving metazoan relationships. This optimized data set is amenable to the most appropriate and computationally intensive analyses using site-heterogeneous models of sequence evolution. We also employed several strategies to examine the potential for long-branch attraction to bias our inferences. Our analyses strongly support the Ctenophora as the sister lineage to other Metazoa. We find no support for the traditional view uniting the ctenophores and Cnidaria. Our findings are supported by Bayesian comparisons of topological hypotheses and we find no evidence that they are biased by long-branch attraction.

CONCLUSIONS

Our study further clarifies relationships among early branching metazoan lineages. Our phylogeny supports the still-controversial position of ctenophores as sister group to all other metazoans. This study also provides a workflow and computational tools for minimizing systematic bias in genome-based phylogenetic analyses. Future studies of metazoan phylogeny will benefit from ongoing efforts to sequence the genomes of additional invertebrate taxa that will continue to inform our view of the relationships among the major lineages of animals.

Elusive ditrysian phylogeny: an account of combining systematized morphology with molecular data (Lepidoptera)

BACKGROUND

Ditrysia comprise close to 99 % of all butterflies and moths. The evolutionary relationships among the ditrysian superfamilies have received considerable attention in phylogenetic studies based on DNA and transcriptomic data, but the deepest divergences remain for large parts unresolved or contradictory. To obtain complementary insight into the evolutionary history of the clade, and to test previous hypotheses on the subdivision of Ditrysia based on morphology, we examine the morphology of larvae, pupae and adult males and females of 318 taxa representing nearly all ditrysian superfamilies and families. We present the most comprehensive morphological dataset on Ditrysia to date, consisting of over 500 morphological characters. The data are analyzed alone and combined with sequence data (one mitochondrial and seven nuclear protein-coding gene regions, sequenced from 422 taxa). The full dataset consists of 473 exemplar species. Analyses are performed using maximum likelihood methods, and parsimony methods for the morphological dataset. We explore whether combining morphological data and DNA-data can stabilize taxa that are unstable in phylogenetic studies based on genetic data only.

RESULTS

Morphological characters are found phylogenetically informative in resolving apical nodes (superfamilies and families), but characters serving as evidence of relatedness of larger assemblages are few. Results include the recovery of a monophyletic Tineoidea, Sesioidea and Cossoidea, and a stable position for some unstable taxa (e.g. Epipyropidae, Cyclotornidae, Urodoidea + Schreckensteinioidea). Several such taxa, however, remain unstable even though morphological characters indicate a position in the tree (e.g. Immidae). Evidence supporting affinities between clades are suggested, e.g. a novel larval synapomorphy for Tineidae. We also propose the synonymy of Tineodidae with Alucitidae, syn. nov.

CONCLUSIONS

The large morphological dataset provides information on the diversity and distribution of morphological traits in Ditrysia, and can be used in future research on the evolution of these traits, in identification keys and in identification of fossil Lepidoptera. The "backbone" of the phylogeny for Ditrysia remains largely unresolved. As previously proposed as an explanation for the scarcity of molecular signal in resolving the deeper nodes, this may be due to the rapid radiation of Ditrysia in the Cretaceous.

Rediscovered parasitism of Andrena savignyi Spinola (Hymenoptera, Andrenidae) by Stylops (Strepsiptera, Stylopidae) and revised taxonomic status of the parasite

Parasitism of Andrena (Suandrena) savignyi Spinola (Hymenoptera: Andrenidae) by Stylops Kirby (Strepsiptera: Stylopidae) has been recorded only once, and from an individual collected in Egypt almost a century ago, with the parasite described as Stylops savignyi Hofeneder. The recent rediscovery of this Stylops from an individual of Andrena savignyi permits a reinterpretation of the species and its affinities among other Stylops. The bee was collected at flowers of Zilla spinosa (Turra) Prantl. (Brassicaceae) in Amariah, Riyadh, Kingdom of Saudi Arabia. Based on DNA barcode sequences from material sampled across Africa, Asia, and Europe, it is apparent that Stylops savignyi is conspecific with Stylops nassonowi Pierce, and we accordingly synonymize this name (syn. n.), with the latter representing the senior and valid name for the species. A differential diagnosis is provided for Stylops nassonowi and the morphology of the female is described, as well as the first instars.

(7E,11E)-3,5,9,11-Tetramethyltridecadienal: Sex Pheromone of the Strepsipteran Xenos peckii

Xenos peckii is a strepsipteran parasitoid of the common North American paper wasp, Polistes fuscatus. Mate-seeking X. peckii males respond to a long-range sex pheromone emitted by the female, which remains permanently embedded within the abdomen of a mobile host wasp. During peak pheromone signalling, we excised the female from her host, severed the cephalothorax containing the pheromone gland, extracted it in hexane, and analyzed aliquots of combined extracts by coupled gas chromatographic-electroantennographic detection (GC-EAD). These analyses revealed a candidate pheromone component (CPC) that consistently elicited strong responses from male antennae. We identified the CPC as (7E,11E)-3,5,9,11-tetramethyltridecadienal based on its retention indices (RI) on three GC-columns, RI inter-column differentials, mass and NMR spectra, and synthesis of an authentic standard that matched the GC-retention and spectrometric characteristics of the CPC. For a field experiment, we prepared (7E,11E)-3,5,9R,11-tetramethyltridecadienal and (7E,11E)-3,5,9S,11-tetramethyltridecadienal. Xenos peckii males were caught in traps baited with either compound singly or a 1:1 mixture of the two but not in unbaited control traps. The sex pheromone of X. peckii resembles that reported for the strepsipterans Stylops mellittae and S. muelleri, (R,R,R)-3,5,9-trimethyldodecanal, suggesting a common biosynthetic pathway across taxonomic genera.

Insect phylogenomics

Phylogenomics, the integration of phylogenetics with genome data, has emerged as a powerful approach to study the evolution and systematics of species. Recently, several studies employing phylogenomic tools have provided better insights into insect evolution. Next-generation sequencing methods are now increasingly used by entomologists to generate genomic and transcript sequences of various insect species and strains. These data provide opportunities for comparative genomics and large-scale multigene phylogenies of diverse lineages of insects. Phy-logenomic investigations help us to better understand systematic and evolutionary relationships of insect species that play important roles as herbivores, predators, detritivores, pollinators and disease vectors. It is important that we critically assess the prospects and limitations of phylogenomic methods. In this review, I describe the current status, outline the major challenges and remark on potential future applications of phylogenomic tools in studying insect systematics and evolution.

Resolving the phylogeny of a speciose spider group, the family Linyphiidae (Araneae)

For high-level molecular phylogenies, a comprehensive sampling design is a key factor for not only improving inferential accuracy, but also for maximizing the explanatory power of the resulting phylogeny. Two standing problems in molecular phylogenies are the unstable placements of some deep and long branches, and the phylogenetic relationships shown by robust supported clades conflict with recognized knowledge. Empirical and theoretical studies suggest that increasing taxon sampling is expected to ameliorate, if not resolve, both problems; however, sometimes neither the current taxonomic system nor the established phylogeny can provide sufficient information to guide additional sampling design. We examined the phylogeny of the spider family Linyphiidae, and selected ingroup species based on epigynal morphology, which can be reconstructed in a phylogenetic context. Our analyses resulted in seven robustly supported clades within linyphiids. The placements of four deep and long branches are sensitive to variations in both outgroup and ingroup sampling, suggesting the possibility of long branch attraction artifacts. Results of ancestral state reconstruction indicate that successive state transformations of the epigynal plate are associated with early cladogenetic events in linyphiid diversification. Representatives of different subfamilies were mixed together within well supported clades and examination revealed that their defining characters, as per traditional taxonomy, are homoplastic. Furthermore, our results demonstrated that increasing taxon sampling produced a more informative framework, which in turn helps to study character evolution and interpret the relationships among linyphiid lineages. Additional defining characters are needed to revise the linyphiid taxonomic system based on our phylogenetic hypothesis.

Error, signal, and the placement of Ctenophora sister to all other animals

Elucidating relationships among early animal lineages has been difficult, and recent phylogenomic analyses place Ctenophora sister to all other extant animals, contrary to the traditional view of Porifera as the earliest-branching animal lineage. To date, phylogenetic support for either ctenophores or sponges as sister to other animals has been limited and inconsistent among studies. Lack of agreement among phylogenomic analyses using different data and methods obscures how complex traits, such as epithelia, neurons, and muscles evolved. A consensus view of animal evolution will not be accepted until datasets and methods converge on a single hypothesis of early metazoan relationships and putative sources of systematic error (e.g., long-branch attraction, compositional bias, poor model choice) are assessed. Here, we investigate possible causes of systematic error by expanding taxon sampling with eight novel transcriptomes, strictly enforcing orthology inference criteria, and progressively examining potential causes of systematic error while using both maximum-likelihood with robust data partitioning and Bayesian inference with a site-heterogeneous model. We identified ribosomal protein genes as possessing a conflicting signal compared with other genes, which caused some past studies to infer ctenophores and cnidarians as sister. Importantly, biases resulting from elevated compositional heterogeneity or elevated substitution rates are ruled out. Placement of ctenophores as sister to all other animals, and sponge monophyly, are strongly supported under multiple analyses, herein.

Partial dosage compensation in Strepsiptera, a sister group of beetles

Sex chromosomes have evolved independently in many different taxa, and so have mechanisms to compensate for expression differences on sex chromosomes in males and females. Different clades have evolved vastly different ways to achieve dosage compensation, including hypertranscription of the single X in male Drosophila, downregulation of both X's in XX Caenorhabditis, or inactivation of one X in female mammals. In the flour beetle Tribolium, the X appears hyperexpressed in both sexes, which might represent the first of two steps to evolve dosage compensation along the paths mammals may have taken (i.e., upregulation of X in both sexes, followed by inactivation of one X in females). Here we test for dosage compensation in Strepsiptera, a sister taxon to beetles. We identify sex-linked chromosomes in Xenos vesparum based on genomic analysis of males and females, and show that its sex chromosome consists of two chromosomal arms in Tribolium: The X chromosome that is shared between Tribolium and Strepsiptera, and another chromosome that is autosomal in Tribolium and another distantly related Strepsiptera species, but sex-linked in X. vesparum. We use RNA-seq (RNA sequencing) to show that dosage compensation along the X of X. vesparum is partial and heterogeneous. In particular, genes that are X-linked in both beetles and Strepsiptera appear fully dosage compensated probably through downregulation in both sexes, whereas genes on the more recently added X segment have evolved only partial dosage compensation. In addition, reanalysis of published RNA-seq data suggests that Tribolium has evolved dosage compensation, without hypertranscribing the X in females. Our results demonstrate that patterns of dosage compensation are highly variable across sex-determination systems and even within species.

From Fossil Parasitoids to Vectors: Insects as Parasites and Hosts

Within Metazoa, it has been proposed that as many as two-thirds of all species are parasitic. This propensity towards parasitism is also reflected within insects, where several lineages independently evolved a parasitic lifestyle. Parasitic behaviour ranges from parasitic habits in the strict sense, but also includes parasitoid, phoretic or kleptoparasitic behaviour. Numerous insects are also the host for other parasitic insects or metazoans. Insects can also serve as vectors for numerous metazoan, protistan, bacterial and viral diseases. The fossil record can report this behaviour with direct (parasite associated with its host) or indirect evidence (insect with parasitic larva, isolated parasitic insect, pathological changes of host). The high abundance of parasitism in the fossil record of insects can reveal important aspects of parasitic lifestyles in various evolutionary lineages. For a comprehensive view on fossil parasitic insects, we discuss here different aspects, including phylogenetic systematics, functional morphology and a direct comparison of fossil and extant species.